We introduce an end-to-end approach to learn the evolution operators of large-scale non-linear dynamical systems, such as those describing complex natural phenomena. Evolution operators are particularly well-suited for analyzing systems that exhibit spatio-temporal patterns and have become a key analytical tool across various scientific communities. As terabyte-scale weather datasets and simulation tools capable of running millions of molecular dynamics steps per day are becoming commodities, our approach provides an effective tool to make sense of them from a data-driven perspective. The core of it lies in a remarkable connection between self-supervised representation learning methods and the recently established learning theory of evolution operators. We deploy our approach across multiple scientific domains: explaining the folding dynamics of small proteins, the binding process of drug-like molecules in host sites, and autonomously finding patterns in climate data. Our code is available open-source at: https://github.com/pietronvll/encoderops.